LLM Mart Basic

Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCOD

Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models,

Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.

Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build over

Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domai

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE a

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene const

Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a gene is expressed in a tissue, correlate regulatory elements with expression, or validate ENCODE findings against GTEx. Trigger on: GTEx, tissue expression, gene e

Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, gen

Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolut

Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal cor

Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif datab

Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver for BED files, CrossMap for VCF/bigWig, and handles unmapped regions with provenance logging.

Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is DNA methylated/unmethylated in my tissue?" by combining per-CpG methylation data

Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite. Use when users need to discover TF binding motifs in peaks, validate ChIP-seq targets, or find co-binding partners. Trigger on: motif analysis, HOMER, MEME, de

Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and whi

Guide for annotating ENCODE peaks with genomic features using ChIPseeker and GREAT. Use when users need to assign peaks to genes, determine genomic feature distribution (promoter, intron, intergenic), or perform gene ontology enrichment of peak-associated genes. Trigger on: peak

Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosom

Discovery worked. Ping worked. Every TCP connection timed out, and later the tunnel only worked when someone had a terminal open.

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Use MCP Inspector to connect to local or remote servers, inspect capabilities, call tools, read resources, test prompts, and diagnose failures before release.

Build an MCP server in TypeScript with focused tools, validated schemas, local and remote transports, Inspector tests, and production security controls.

Turn a GAIA workflow misfire into a redacted, classified, filing-ready bug report in one read-only pass. Self-diagnoses config issues inline; files probable bugs upstream on confirmation.

Judge-the-form, human-gated hardening. Reviews recurring code-audit-frontend findings and, with approval, drafts the lowest-context-weight form (deterministic check / skill / path-scoped prose rule) into the working tree. Pass `list` to see live candidates or `why <finding_class>` to explain one.

Initialize a new project from the GAIA React template, renames, strips GAIA branding, configures i18n, installs Claude skills/plugins.

Plan a complex feature using GAIA's task-orchestration pattern, structures the work into fresh-context subagent phases for your approval. Does not implement.

Cut a new GAIA release, bump version, graduate CHANGELOG, regenerate manifest, open release PR, then tag on merge. Maintainer-only.

Detect and, on explicit consent, additively append the languages Serena is not indexing to the `languages:` list in `.serena/project.yml`, then prompt a Serena restart. Never mutates without a yes; inert without Serena.

Author an immutable SPEC artifact through Socratic discovery (spec-kit wrapper), then STOP. Terminal, never runs /gaia-plan; it prints a /gaia-plan prompt the human pastes into a fresh session. Pass `auto <description>` for non-interactive mode that answers its own questions.

Maintainer-only autonomous health audit + auto-heal loop. Runs N=3 fresh-team audit-fix-audit cycles with circuit breakers, reports an F-to-A+ verdict (folding in the shared Claude-integration fitness grade) or escalates.

Single post-init onboarding command; detects situation, runs only owed phases; safe to re-run. --reconfigure rotates token and re-selects tools.

GAIA before_specify hook: constitution placeholder check + spec-kit version-pin drift detection.

GAIA after_specify hook: immutability lint over the just-written SPEC artifact.

Close a plan after implementation+merge. Offers wiki-promote for the plan's consolidated SUMMARY.md, cold-consolidates an out-of-band merge, then early-reaps the local plan folder once cost is represented in cost.jsonl.

GAIA self-review: pre-gate-2 review pass on the in-progress SPEC draft.

Close a SPEC after implementation+merge. Optional drain of deferred wiki-promote, cold-consolidates an out-of-band merge into SUMMARY.md, then early-reaps the local SPEC folder once cost is represented in cost.jsonl.

GAIA Socratic discovery wrapper: /speckit-specify for the initial draft, then GAIA's own Socratic clarify loop.

GAIA before_implement hook: render PO-authored UATs into Playwright e2e specs at .playwright/e2e/spec-NNN/.

Promote merged SPEC or plan content into the GAIA wiki.

This project uses the GAIA preset. Bare `/speckit-clarify` is not the clarify path here: core clarify writes an off-shape artifact (a `## Clarifications` / `### Session` block with five-word answers) and carries a question cap GAIA does not use. Run `/gaia-spec` instead — it driv

GAIA-wrapped /speckit-specify: writes through core, then relocates the artifact to .gaia/local/specs/SPEC-NNN/SPEC.md and stamps GAIA frontmatter.

Show or configure the compact Fallow Impact statusline in Claude Code

Unofficial KakaoTalk CLI and native MCP server for macOS — read, watch, and send messages via Accessibility automation.

Local-first AI action assistant for operators: memory, skills, tools, and permission gates to turn work into controlled action.

Agent-driven media library for your cloud drives (Quark 夸克 / 115 / 光鸭 GuangYa / 123网盘 / 天翼 Tianyi)

An open-source desktop AI agent built around Cyrene’s persona and powered by the self-developed Cyrene_Harness framework. It combines immersive character chat w…

在 Android 上运行的 AI 编程 Agent，内置 Linux 终端与代码编辑器，支持 MCP 协议扩展。

TencentDB Agent Memory is a team-level memory hub for AI Agents — turning conversations, docs, and code into four reusable memory assets (Chat Memory, Skill, LL…

Floe — a native iOS/iPadOS AI agent workspace for iPhone and iPad, built for private bring-your-own-key workflows.

Spring Boot AI Agent — an out-of-the-box solution that makes your app converse, remember, think, and act.

Give your AI agent eyes for PDFs — structured text, tables, OCR, visual evidence, and page-level citations via MCP. Native Rust, local-first.

A tiny Claude Code skill that keeps your prompt cache warm during idle sessions, so your next message reads from cache instead of paying full price.

Monet — Multi-engine mission control for coding agents (Claude Code and Codex today). Browse, search, and drive your agent sessions from a native desktop app.

A DottedSign MCP server that enables AI assistants (Claude, ChatGPT) to manage signing tasks, templates, and document status via natural language.

Курируемый handbook по Claude Code на русском: hooks, skills, CLAUDE.md шаблоны, MCP-серверы, кейсы.

👾 Open Computer Use – Open-Source Alternative to Codex Computer Use

An open-source AI companion that actually remembers you — runs entirely on your own Mac or server. Desktop pet · long-term memory · proactive companionship · mu…

Graphical management tool for Kubernetes on desktop and mobile.

Open-source desktop app for content creation, with an agent runtime and standalone CLI.

Connect Claude and ChatGPT to KDAN PDF — upload, edit, compress, protect, redact, and compare PDFs in chat.

Ekko Studio is a local-first AI workspace for multi-agent chat, coding, and visual workflows, available on desktop and the web.

Open-source native iPhone/iPad client for OpenAI Codex CLI and Claude Code — review diffs, approve actions, steer sessions, and manage Git remotely.